Familia was posthumously promoted to Detective First-Grade before the service, which occurred 12 years to the day that she officially joined the NYPD.
New York City Mayor Bill de Blasio told the mourners that Familia died "solely because she wore a uniform" and called on everyone to stop violence against police officers.
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"We've watched with horror these attacks on our police here in New York City and all around our country. It sickens us, and we know they cannot be tolerated, and we know they must end," de Blasio said. "She loved this city and she loved this country because she understood its magic. She saw what was possible, what it meant for herself, for her children. She lived for them, but she died for all of us."
WATCH: Mayor de Blasio speaks at funeral
Mayor de Blasio: Officer Familia died because she wore a uniform
Police Commissioner James O'Neill said Familia's death "should remind everybody that the civility of our city rests on a knife's edge."
"Where are the demonstrations for the single mom who cared for her elderly mother and three children?" he asked to a thunderous, extended standing ovation from an audience packed with officers. "There is anger and sorrow, but why is there no outrage?"
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He called safety and order a shared responsibility between police and residents and pressed the public "to make a commitment to help your police, to work with us.
Familia's 20-year-old daughter, Genesis Vilella, said she was also a "protector, defender, guidance counselor, spiritual adviser ... philosopher, philanthropist, theorist and mother."
WATCH: Familia's children speak at funeral
Children of Miosotis Familia speak at funeral
New York Gov. Andrew Cuomo paid his respects to Familia at the wake on Monday.
Familia, 48, was assassinated in a police vehicle parked inside a crime-ridden Bronx precinct last Wednesday (July 5) when 34-year-old Alexander Bonds walked up to the vehicle and fired once through the passenger window, striking Familia in the head. Bonds ran from the scene but police caught up to him and opened fire, killing him after they said he turned the gun on them. Bonds had sought psychiatric care just days earlier.
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Familia came on the job in 2005, after working as a patient care assistant at New York University Hospital, and also for the American Red Cross. She spent her entire career in the Bronx precinct where she was killed.
She has a 20-year-old daughter and 12-year-old twins, a boy and a girl. She also was caring for her 86-year-old mother.
Familia is the first female officer to die in the line of duty since 9/11.
(Some information from the Associated Press)